"This official version departed from the facts of the day in four critical respects.
First, the official version indicated that the Langley fighters were scrambled in response to American 77, and thus omitted completely the pivotal report of the morning and the source of the Langley scramble: the report that American 11, the first hijack, was still airborne and heading for Washington.
Second, the administration insisted that the military was tracking United 93 and, as a consequence, was positioned to intercept the flight if it approached Washington. This was untrue; the military could not locate the flight to track it because it had crashed by the time of notification.
Third, the official version insisted that President Bush had issued an authorization to shoot down hijacked commercial flights, and that the order had been processed through the chain of command and passed to the fighters. This was untrue.
Fourth, the administration version implied, where it did not state implicitly, that the chain of command had been functioning on 9/11, and that the critical decisions had been made by the appropriate top officials. Thus, the president issued the shoot-down order; top FAA Headquarters officials coordinated closely with the military; Transportation secretary Norman Mineta issued the order to land all airplanes; NORAD Commanding General Eberhart monitoring closely the decisions taken at NEADS and CONR; and so on. None of this captures how things actually unfolded on the day.
Page 255, The Ground Truth, John Farmer